I'll give this a shot, however it's worth noting that these probably change everytime I listen through the albums:
WDADU - Toss up between The Killing hand and Light Fuse.
I&W - Very hard choice between Learning to Live and Metropolis and even Glass Moon but uh, if I can say Wait for Sleep/Learning to live as one answer then that.
Awake - Voices hands down (Or better yet, the whole A Mind Beside Itself). The Mirror's up there but most of this album is amazing anyway.
FII - New Millennium, Lines in the Sand, those two are tops.
SFAM - Beyond this Life, not much else to say, the rest works with the whole but this one stands out. Wait... Home too.
6DOIT - The Glass Prison 'nuff said.
TOT - Honor Thy Father, yeah seriously.
8vm- Octavarium and Root are about equal.
SC - Constant Motion.
BC&SL - A Rite of Passage = The Count of Tuscany.
ADTOE - Breaking all Illuions = Beneath the Surface.
DT - Illumination Theory = The Bigger Picture.
For the last 3, I equally enjoy both despite the fact that they're generally quite different and wouldn't normally get compared. So it was impossible to rank accurately therefore I decided I like each of them about the same amount.